Abstract:
BACKGROUND: Mitochondrial DNA (mtDNA) has long been used to date
historical demographic events. The idea that it is useful for molecular
dating rests on the premise that its evolution is neutral. Even though
this idea has long been challenged, the evidence against clock-like
evolution of mtDNA is often ignored. Here, we present a particularly
clear and simple example to illustrate the implications of violations of
the assumption of selective neutrality.
METHODS: DNA sequences were generated for the mtDNA COI gene
and the nuclear 28S rRNA of two closely related rocky shore snails,
and species-level variation was compared. Nuclear rRNA is not usually
used to study intraspecific variation in species that are not spatially
structured, presumably because this marker is assumed to evolve so
slowly that it is more suitable for phylogenetics.
RESULTS: Even though high inter-specific divergence reflected the
faster evolutionary rate of COI, intraspecific genetic variation was
similar for both markers. As a result, estimates of population
expansion times based on mismatch distributions differed between
the two markers by millions of years.
CONCLUSIONS: Assuming that 28S evolution is more clock-like, these
findings can be explained by variation-reducing purifying selection in
mtDNA at the species level, and an elevated divergence rate caused by
diversifying selection between the two species. Although these two
selective forces together make mtDNA suitable as a marker for
species identifications by means of DNA barcoding because they
create a ‘barcoding gap’, estimates of demographic change based on
this marker can be expected to be highly unreliable. Our study
contributes to the growing evidence that the utility of mtDNA
sequence data beyond DNA barcoding is limited.
